The facility is supervised from the Biodome Control Room, but at the time of the Black Mesa Incident, its access is blocked by the collapsed ceiling. Furthermore, Xen and Race X creatures have caused utter chaos around the labs.

The complex contains a series of Specimen Observation Areas where captured Xen aliens and flora are kept and observed in artificial recreations of their natural habitats. Each Area has a Control Room located above, where it can be observed through a wide window.

This area appears as a standard terrestrial area, with grass and rocks. There can be found a dead clean suit scientist and dead Houndeyes. While going there, Shephard is attacked by a Voltigore. Its Control Room cannot be accessed.

This area is still under construction, and two unwanted Tentacles can be found there, as well as more Spore Launcher spores. Its unfinished Control Room can be accessed using an elevator at the exit of Lab BDRC-101. There, only crates full of computer parts can be found. Shephard leaves Sector E through a vent located in Specimen Observation Area 03, and proceeds to Waste Processing Area 3 where he will confront the Pit Worm.

Alongside these enclosures are two Specimen Containment Rooms where aliens are studied in closer detail. One room has three Spore Launchers stored in tanks. One of the tanks is broken, and a Spore Launcher lies on the ground. This is at that point Shephard acquires it. The room also contains Houndeyes and Headcrabs behind glasses. The other room contains, behind glass, Snark nests, a Bullsquid, and more Houndeyes and Headcrabs. A scientist is being zombified, and a Gonome has broken into the room. A small elevator also gives access to Specimen Observation Area 02.

In this lab, Shephard can listen to an holographic message intended to Walter Bennet about their work on the Barnacles and their use as a weapon. In the message, the scientist suggests Bennet take on the work on Specimen 1176.

In that other, dark Specimen Containment Room can be found four glass cases. One, originally containing Specimen 007, is empty and broken, another contains Specimen 1069, a Xen Fungus, another contains specimen 0124, a Light Stalk, and another contains Specimen 1176, the Barnacle Grapple.

In the next room, the Barnacle Gun can be tested on several things: a Headcrab, a Houndeye, a crate, and rocks, the latter being there to show the weapon's inefficiency against non-organic materials. An elevator also leads to the unfinished control room of Specimen Observation Area 03.

In the Specimen Cultivation Room it is learned how to use the Barnacle Gun on Spore Launcher spores to cross deep pits. The second and last Specimen Cultivation Room, located behind the hologram console, contains several Barnacles attached to the ceiling.

The lowest level of Sector E (Level B), linked to the upper areas with an elevator, contains the Hydrofauna Studies Laboratory, where aquatic aliens such as Ichthyosaurs and Leeches are kept and observed by clean suit scientists in older decommissioned areas that have been apparently flooded and converted into makeshift tanks. Two teleports are also used there to easily work inside cages installed among the Ichthyosaurs. At the time of the Black Mesa Incident, the elevator access from the upper levels is obstructed by the collapsed ceiling; it can only be accessed through a hole on the ground leading to the Biodome Drainage System, then to Level B. Adrian Shephard goes through the Sector from Level B, after witnessing Gordon Freeman teleporting to Xen in Sector F.

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A mostly industrial area, the Materials Transport consists of a network of dilapidated monorail trams extending deep beneath the facility. It also features several hangars, ordinance facilities, maintenance areas, and offices.[7][8][9]

Most sections of the Materials Transport feature several trams, partially flooded areas, and prominent Xen wildlife. Some parts are still in use while others are in a dire state of disrepair.

The HECU firmly holds the area near the High Altitude Launch Center. Along the Materials Transport tracks, they have set up several artillery pieces, and are heavily attacked by Vortigaunts. They also write on the wall many taunts directly addressed to Freeman, sometimes rather misspelled.

The Materials Transport includes two types of freight trams: one with a control console at the front and a wooden flatbed for carrying cargo (one is also featured at the end of Sector A's Hazard Course, while it is connected to the Black Mesa Transit System, using different trams); and a bulky, heavy variety presumably used for pulling large volumes of cargo behind it. The latter is used and derails at the very start of the chapter Apprehension, and can also be seen at the start of the game during the tram ride, although there it does not use tracks.

The Materials Transport should not be confused with the Black Mesa Transit System, provided for the security, comfort, and convenience of Black Mesa personnel, residents, and visitors.[8][10]

Part of the lower levels are located under a waste processing area located near a small flooded area under Silo D, where the Tentacles have their roots. This is where Freeman starts his tram ride trough the Materials Transport at the end of the chapter Power Up after battling a Gargantua. There the Sector E Track Control where the G-Man is seen can be found, and it is powered by a partially flooded Power Generator located below and accessed through a large elevator in an area controlled by a large platoon of HECU Soldiers, and that Freeman must restart. This area is isolated from the rest of the network by concrete blocks put on the tracks and is also filled with Vortigaunts and Houndeyes.[8]

One side of level B is used for a Secured Access of the Lambda Sector Transport, linked to Sector F. This area is not controlled by the HECU but by the Black Ops. Located beside the tracks are offices where can be found the offices of S. Jones and S. Reardon (a nod to Gearbox employees Sean Reardon and Steven Jones), a small lobby with a glass roof, a meeting room with a video projector, charts for the Displacer Cannon, and office B-591FG containing a "Employee of the Month" picture of Gordon Freeman. Above the offices and near the building where the tracks can be accessed is also found an Ordinance Storage Facility where the Mark IV Thermonuclear Device is first seen in a truck. The offices are connected to the surface by a deep hole created by an antenna that collapsed, where a generator can be found. One vent found near the tracks directly links to Level A of Sector F, where Shephard witnesses Gordon Freeman's departure to Xen.[7]

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The biggest of the three Ordinance Storage Facilities seen in the four games of the Half-Life story arc, this area covers the Opposing Force chapters "The Package" and Worlds Collide, as well as the Decay bonus chapter Xen Attacks. It is separated from Sector G's Hydro-Electric Dam by a small desert area accessed from the dam by a duct system leading to exit H-287GQ, and connected to Sector E Materials Transport through its underground parking lot. The outside is controlled by the Black Ops that have set up a mortar on one roof, but it is mostly swarmed by Shock Troopers, Voltigores, and Vortigaunts. Inside, the buildings are partially destroyed, and a Black Ops Apache is targeting a Voltigore. On the ground floor and beneath the facility is a multi-story parking lot where the Black Ops are fighting further Race X creatures, and where they set up the thermonuclear warhead that will destroy Black Mesa, finally activated by the G-Man in person. There, VortigauntsR-4913 and X-8973 are also sent earlier by the Nihilanth to retrieve Xen crystal samples in the part of the parking lot located beyond the gate present near the bomb's truck. Under the parking lot is Storage Unit 04, a freight area filled with crates and containers, and accessible from the parking lot by an elevator. The place is also heavily guarded by the Black Ops, also attacked there by Race X creatures. A practically abandoned industrial ventilation tunnel located further underground contains a Race X portal that, when apparently powered by hundreds of Sprites, brings in the Gene Worm soon defeated by Adrian Shephard.

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Visited by Gordon Freeman during the Half-Life chapter Apprehension, this unnamed area connected to the Materials Transport includes partially flooded areas filled with Leeches, and an Ichthyosaur (this is where they are first introduced) - one of them introducing the crossbow and its efficiency against Ichthyosaurs, a cryogenic storage facility, and a storage area where the Black Ops are first introduced. After being captured by the HECU (briefly witnessed by Barney Calhoun when caught in a harmonic reflux before escaping Black Mesa), he wakes up in a garbage compactor near the Biological Waste Processing Plant.

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Level A of this Black Mesa Transit System section can be accessed from the Sector C Line, where the G-Man is first seen in Half-Life, and leads to an unnamed area where the first Shock Trooper and zombie security guards are encountered.[7]

According to early builds of Half-Life, the Sector E Materials Transport area and its tram were originally very different, and apparently not in such a state of disrepair.[11]

The Half-Life texture files feature three signs with "c2a2a" in their names. One has "Sector E Subsurface Transport - Level A" written in blue, another has "Sector E Loading Bay" written in orange, and the third has "Subsurface Materials Transport System" written in red. In the map named "c2a2a," which is the second map of the Half-Life chapter On A Rail, none of these signs can be found. The "Sector E Subsurface Transport" sign can, however, be seen near the Sector C Line in Opposing Force, in the area where the G-Man is first seen in Half-Life, thus bringing this name back into canon, but in another location.

The cryogenic storage facility traversed in the Half-Life chapter Apprehension was originally to feature another room containing Xen specimens and a cooling tank with a puzzle requiring the player to avert a meltdown or an explosion caused by a power surge. The cryogenic tanks featured in the retail game were also to be made of stainless metal, simplified in the final game.[1]

The Half-Life Deathmatch map "subtransit" features an area similar to Sector E Materials Transport, with a similar monorail, but yellow in color and of more modern design.

Under an HECU outpost in the Materials Transport (in the map "c2a2c") can be found an Easter egg placed by the mapper, Dave Riller, consisting of his last name in relief.[12]